Genotyping and gene expression analyses of tissue samples can be of significant importance for the identification of disease biomarkers (e.g., genetic determinants), for the accurate diagnosis of disease, and for the determination of patients′ course of treatment. Pharmacogenomic methods can identify patients likely to respond to a particular drug and lead to new therapeutic approaches. For example, tumor tissue excised from a patient can be analyzed for the increased or decreased expression of particular disease biomarkers and thereby help clinicians identify therapeutic agents that could be useful in treating the patient.
Genotyping and gene expression studies (e.g., by reverse transcriptase polymerase chain reaction (RT-PCR) amplification) of tissue samples often is performed using frozen tissue samples. However, many pathological samples are not prepared as frozen tissues, but rather are formalin-fixed and paraffin-embedded (FFPE) to allow histological analysis and archival storage. Thus, rapid and reliable methods for extracting nucleic acids from paraffin-containing tissue samples would greatly aid the study of disease mechanisms and biomarkers. The inventions disclosed herein address this need.